Zinc in PDB 5k92: Crystal Structure of An Apo Tris-Thiolate Binding Site in A De Novo Three Stranded Coiled Coil Peptide

The structure of Crystal Structure of An Apo Tris-Thiolate Binding Site in A De Novo Three Stranded Coiled Coil Peptide, PDB code: 5k92 was solved by L.Ruckthong, M.L.Zastrow, J.A.Stuckey, V.L.Pecoraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.87 / 1.42
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.574, 29.409, 44.353, 90.00, 118.78, 90.00
R / Rfree (%)	19.5 / 23

The structure of Crystal Structure of An Apo Tris-Thiolate Binding Site in A De Novo Three Stranded Coiled Coil Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of An Apo Tris-Thiolate Binding Site in A De Novo Three Stranded Coiled Coil Peptide (pdb code 5k92). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of An Apo Tris-Thiolate Binding Site in A De Novo Three Stranded Coiled Coil Peptide, PDB code: 5k92:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of An Apo Tris-Thiolate Binding Site in A De Novo Three Stranded Coiled Coil Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of An Apo Tris-Thiolate Binding Site in A De Novo Three Stranded Coiled Coil Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:16.3 occ:0.93 OE2 A:GLU24 2.0 18.1 1.0 CD A:GLU24 2.6 19.2 1.0 OE1 A:GLU24 2.7 16.7 1.0 HE1 A:HIS28 3.4 17.2 1.0 HZ1 C:LYS22 3.5 20.8 1.0 OE1 A:GLU27 3.8 24.4 1.0 HZ2 C:LYS22 3.8 22.2 1.0 O A:HOH203 3.9 27.9 1.0 CG A:GLU24 4.1 16.0 1.0 OE2 A:GLU27 4.1 30.4 1.0 NZ C:LYS22 4.1 20.9 1.0 CD A:GLU27 4.4 25.2 1.0 CE1 A:HIS28 4.4 17.4 1.0 HG2 A:GLU24 4.4 17.2 1.0 HG3 A:GLU24 4.4 16.4 1.0 HZ3 C:LYS22 4.6 18.1 1.0 HA A:GLU24 4.9 16.5 1.0 ZN A:ZN102 5.0 14.4 0.8

Zinc binding site 2 out of 3 in the Crystal Structure of An Apo Tris-Thiolate Binding Site in A De Novo Three Stranded Coiled Coil Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of An Apo Tris-Thiolate Binding Site in A De Novo Three Stranded Coiled Coil Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:14.4 occ:0.80 NE2 A:HIS28 2.0 18.0 1.0 CE1 A:HIS28 3.0 17.4 1.0 CD2 A:HIS28 3.1 18.9 1.0 HE1 A:HIS28 3.2 17.2 1.0 HD2 A:HIS28 3.3 20.4 1.0 ND1 A:HIS28 4.2 18.4 1.0 CG A:HIS28 4.2 18.9 1.0 OE2 A:GLU27 4.6 30.4 1.0 O A:HOH203 4.7 27.9 1.0 OE2 A:GLU24 4.8 18.1 1.0 ZN A:ZN101 5.0 16.3 0.9 HG2 A:GLU27 5.0 22.9 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of An Apo Tris-Thiolate Binding Site in A De Novo Three Stranded Coiled Coil Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of An Apo Tris-Thiolate Binding Site in A De Novo Three Stranded Coiled Coil Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:23.8 occ:0.67 NE2 C:HIS28 2.1 18.7 0.7 CE1 C:HIS28 3.0 19.8 0.7 CD2 C:HIS28 3.1 19.4 0.7 HE1 C:HIS28 3.2 21.3 0.7 HD2 C:HIS28 3.4 20.7 0.7 O C:HOH201 4.0 32.0 1.0 ND1 C:HIS28 4.2 22.7 1.0 CG C:HIS28 4.2 22.0 1.0 O2 C:PEG103 4.2 44.3 1.0 C2 C:PEG103 4.5 45.2 1.0

L.Ruckthong, M.L.Zastrow, J.A.Stuckey, V.L.Pecoraro. A Crystallographic Examination of Predisposition Versus Preorganization in De Novo Designed Metalloproteins. J.Am.Chem.Soc. V. 138 11979 2016.
ISSN: ESSN 1520-5126
PubMed: 27532255
DOI: 10.1021/JACS.6B07165